Mycobacterium tuberculosis NAD+-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I

DNA ligases are important enzymes which catalyze the joining of nicks between adjacent bases of double-stranded DNA. NAD+-dependent DNA ligases (LigA) are essential in bacteria and are absent in humans. They have therefore been identified as novel, validated and attractive drug targets. Using virtual screening against an in-house database of compounds and our recently determined crystal structure of the NAD+ binding domain of the Mycobacterium tuberculosis LigA, we have identified N1, N(n)-bis-(5-deoxy-alpha-D-xylofuranosylated) diamines as a novel class of inhibitors for this enzyme. Assays involving M.tuberculosis LigA, T4 ligase and human DNA ligase I show that these compounds specifically inhibit LigA from M.tuberculosis. In vitro kinetic and inhibition assays demonstrate that the compounds compete with NAD+ for binding and inhibit enzyme activity with IC50 values in the microM range. Docking studies rationalize the observed specificities and show that among several glycofuranosylated diamines, bis xylofuranosylated diamines with aminoalkyl and 1, 3-phenylene carbamoyl spacers mimic the binding modes of NAD+ with the enzyme. Assays involving LigA-deficient bacterial strains show that in vivo inhibition of ligase by the compounds causes the observed antibacterial activities. They also demonstrate that the compounds exhibit in vivo specificity for LigA over ATP-dependent ligase. This class of inhibitors holds out the promise of rational development of new anti-tubercular agents.     

Modulation of osmotic stress effects on photosynthesis and respiration by temperature in mesophyll protoplast of pea

Exposure of mesophyll protoplast of pea to osmotic stress decreases the rate of photosynthesis while stimulating marginally the respiratory rate of mesophyll protoplasts. The interaction of osmotic and temperature stress during the modulation of photosynthetic and respiratory rates of pea (Pisum sativum var Azad P1) mesophyll protoplasts was investigated. The protoplasts were exposed to either iso-osmotic (0.4 M) or hyper-osmotic (1.0 M) concentration of sorbitol at 15 degrees and 25 degrees C. The rates of photosynthesis and respiration were studied. At optimum temperature of 25 degrees C, there was a decrease in photosynthesis (< 10%) at hyper-osmoticum (osmotic effect), whereas respiration increased marginally (by about 15%). Low temperature (15 degrees C) aggravated the sensitivity of both respiration and photosynthesis to osmotic stress. At 15 degrees C, the decrease in photosynthesis due to osmotic stress was > 35%, while the respiratory rate was stimulated by 30%. The relative proportion of cytochrome pathway decreased by about 50% at both 15 degrees C and 25 degrees C while that of alternative pathway increased, more so, at 15 degrees C, when the mesophyll protoplasts were subjected to hyper-osmoticum stress. The titration experiments showed that extent of engagement of alternative pathway was higher, the slope value was slightly higher for 15 degrees C compared to 25 degrees C. Low temperature modulates the effect of hyper-osmoticum stress on photosynthesis and respiration, and results in increased participation of alternative pathway.     

A D-amino acid editing module coupled to the translational apparatus in archaea

We report the crystal structure of an archaea-specific editing domain of threonyl-tRNA synthetase that reveals a marked structural similarity to D-amino acid deacylases found in eubacteria and eukaryotes. The domain can bind D-amino acids despite a low sequence identity to other D-amino acid deacylases. These results together indicate the presence of these deacylases in all three kingdoms of life. This underlines an important role they may have played in enforcing homochirality during translation.     

Laboratory and field scale bioremediation of hexachlorocyclohexane (HCH) contaminated soils by means of bioaugmentation and biostimulation

Hexachlorocyclohexane (HCH) contaminated soils were treated for a period of up to 64 days in situ (HCH dumpsite, Lucknow) and ex situ (University of Delhi) in line with three bioremediation approaches. The first approach, biostimulation, involved addition of ammonium phosphate and molasses, while the second approach, bioaugmentation, involved addition of a microbial consortium consisting of a group of HCH-degrading sphingomonads that were isolated from HCH contaminated sites. The third approach involved a combination of biostimulation and bioaugmentation. The efficiency of the consortium was investigated in laboratory scale experiments, in a pot scale study, and in a full-scale field trial. It turned out that the approach of combining biostimulation and bioaugmentation was most effective in achieving reduction in the levels of α- and β-HCH and that the application of a bacterial consortium as compared to the action of a single HCH-degrading bacterial strain was more successful. Although further degradation of β- and δ-tetrachlorocyclohexane-1,4-diol, the terminal metabolites of β- and δ-HCH, respectively, did not occur by the strains comprising the consortium, these metabolites turned out to be less toxic than the parental HCH isomers.     

Secretome,surfome and immunome: emerging approaches for the discovery of new vaccine candidates against bacterial infections

Functional genomics has made possible advanced structure-to-function investigation of pathogens and helped characterize virulence mechanisms. Proteomics has been become a tool for large-scale identification of proteins involved during invasion and infection by the pathogens. Bacterial surface and secreted proteins play key role in the interaction between the bacterial cell and the host environment. Thus exoproteome and surface proteome of a microorganism are hypothesized to contain components of effective vaccines. Surfome and exoproteome analysis strategy facilitates identification of novel vaccine antigen and overall helps in progress of discovery of vaccine. The study of the antibody response can advance how proteomics is used, because it investigates antibody–antigen interactions and also unravel the relationship of antibody responses to pathogen and host characteristics. System immunology integrating with proteome i.e. immunoproteomics is applicable to those infections that are having tendency of diverse antibody target recognition and thus accurately reflects progression of the infection.     

Marker-assisted introgression of the major bacterial blight resistance gene, <Emphasis Type="Italic">Xa21</Emphasis> and blast resistance gene, <Emphasis Type="Italic">Pi54</Emphasis> into RPHR-1005, the restorer line of the popular rice hybrid,DRRH3

The elite Indian rice hybrid, DRRH3 is highly susceptible to two major diseases, bacterial blight (BB) and blast, which limit its productivity significantly. In the present study, we have introgressed two major genes, viz., Xa21 and Pi54 conferring resistance against BB and blast, respectively into RPHR-1005, the male parent of DRRH3 through marker-assisted backcross breeding (MABB) and analyzed the backcross derived plants for their resistance against BB and blast. RPBio Patho-2 was used as a donor for both the resistance genes. Gene-specific markers were used for the foreground selection of Xa21 and Pi54 at each stage of backcrossing and markers specific for the major fertility restorer genes, Rf3 and Rf4 were used only at BC₁F₁ generation for foreground selection. Background selection was done using 62 polymorphic SSR markers and marker-assisted backcrossing was continued till BC₃ generation. At BC₃F₄, through intensive phenotype-based selections 15 promising lines (ABLs) possessing high level of resistance against BB and blast, high yield, fine-grain type, complete fertility restoration along with better panicle exsertion and taller plant type as compared to RPHR-1005 were identified and test crossed with APMS 6 A, the female parent of DRRH3. The newly derived hybrids (i.e. improved versions of DRRH3) were observed to possess high level of resistance against BB and blast along with medium-slender grain type and yield level better than or equivalent to that of DRRH3. Our study exemplifies the utility of MABB for targeted improvement of multiple traits in hybrid rice.     

Strategies to Improve Child Immunization via Antenatal Care Visits in India: A Propensity Score Matching Analysis

Numerous studies have examined the empirical evidence concerning the influence of demographic and socio-economic factors influencing child immunization, but no documentation is available which shows the actual impact of antenatal care (ANC) visits on subsequent child immunization. Therefore, this paper aims to examine the net impact of ANC visits on subsequent utilization of child immunization after removing the presence of selection bias. Nationwide data from India’s latest National Family Health Survey conducted during 2005–06 is used for the present study. The analysis has been carried out in the two separate models, in the first model 1–2 ANC visit and in the second model three or more ANC visits has been compared with no visit. We have used propensity score matching method with a counterfactual model that assesses the actual ANC visits effect on treated (ANC visits) and untreated groups (no ANC visit), and have employed Mantel-Haenszel bounds to examine whether result would be free from hidden bias or not. Using matched sample analysis result shows that child immunization among the groups of women who have completed 1–2 ANC visits and those who had more than two visits was about 13 percent and 19 percent respectively, higher than the group of women who have not made any ANC visit. Findings of nearest neighbor matching with replacement method, which completely eliminated the bias, indicate that selection bias present in data set leads to overestimates the positive effects of ANC visits on child immunization. Result based on Mantel-Haenszel bounds method suggest that if around 19 percent bias would be involved in the result then also we could observe the true positive effect of 1–2 ANC visits on child immunization. This also indicates that antenatal clinics are the conventional platforms for educating pregnant women on the benefits of child immunization.